DUF501 - PFAM28P - GREMLIN Contacts

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DUF501 - Protein of unknown function (DUF501)

PFAM:	PF04417	Sequences: VAVRCPCGLPAVVETAPRRRGLPDGTPFPTLYYLTCPRLVAAVSRLEAAGGMREMEARLAADPELAAAYAAAHERYLAERDALAPAAGGGPVEELGPDPEIPGGGAGGMPDPDRVKCLHAHVAHALAGPGVNPVGDEVLE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	140 (126)
Sequences:	4899 (2310)
Seq/√Len:	205.8
META:	0.868

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_V	122_V	3.805	1.00
3_V	11_A	3.569	1.00
58_R	137_E	2.807	1.00
122_V	139_L	2.788	1.00
32_Y	79_E	2.485	1.00
14_E	79_E	2.369	1.00
57_A	61_A	2.339	1.00
122_V	138_V	2.319	1.00
75_R	79_E	2.271	1.00
36_C	39_L	2.226	1.00
5_C	36_C	2.090	1.00
59_L	69_Y	2.041	1.00
70_A	74_E	2.027	1.00
13_V	35_T	2.006	1.00
51_G	54_E	1.974	1.00
55_M	137_E	1.908	1.00
124_H	132_N	1.719	1.00
68_A	136_D	1.686	1.00
31_L	83_L	1.647	1.00
31_L	79_E	1.642	1.00
58_R	65_L	1.622	1.00
40_V	44_S	1.618	1.00
74_E	78_A	1.587	1.00
18_R	84_A	1.576	1.00
125_A	136_D	1.570	1.00
34_L	39_L	1.569	1.00
5_C	9_L	1.568	1.00
122_V	125_A	1.558	1.00
14_E	31_L	1.525	1.00
75_R	124_H	1.524	1.00
9_L	36_C	1.490	1.00
75_R	128_G	1.484	1.00
125_A	139_L	1.483	1.00
41_A	45_R	1.463	1.00
2_A	14_E	1.439	1.00
11_A	36_C	1.430	1.00
124_H	128_G	1.399	1.00
71_A	74_E	1.395	1.00
55_M	134_V	1.329	1.00
41_A	44_S	1.323	1.00
2_A	127_A	1.304	1.00
65_L	134_V	1.294	1.00
85_P	88_G	1.285	1.00
54_E	58_R	1.250	1.00
42_A	45_R	1.246	1.00
128_G	131_V	1.242	1.00
11_A	39_L	1.202	1.00
39_L	122_V	1.201	1.00
124_H	130_G	1.198	1.00
88_G	91_P	1.195	1.00
38_R	42_A	1.181	1.00
71_A	75_R	1.179	1.00
107_G	120_A	1.179	1.00
58_R	62_D	1.177	1.00
69_Y	73_H	1.176	1.00
74_E	77_L	1.165	1.00
66_A	70_A	1.160	1.00
131_V	136_D	1.156	1.00
34_L	43_V	1.155	1.00
72_A	133_P	1.147	1.00
34_L	123_A	1.142	1.00
68_A	71_A	1.113	1.00
79_E	82_A	1.100	1.00
46_L	138_V	1.063	1.00
22_L	26_T	1.045	1.00
78_A	82_A	1.027	1.00
76_Y	124_H	1.004	1.00
43_V	138_V	0.972	1.00
37_P	40_V	0.969	1.00
79_E	128_G	0.963	1.00
73_H	109_M	0.961	1.00
73_H	106_A	0.958	0.99
60_A	113_D	0.943	0.99
73_H	114_R	0.932	0.99
70_A	113_D	0.921	0.99
134_V	137_E	0.917	0.99
121_H	134_V	0.914	0.99
55_M	58_R	0.912	0.99
64_E	67_A	0.910	0.99
7_C	38_R	0.903	0.99
75_R	131_V	0.888	0.99
63_P	67_A	0.873	0.99
65_L	137_E	0.867	0.99
45_R	49_A	0.859	0.99
68_A	133_P	0.855	0.99
46_L	51_G	0.835	0.99
18_R	100_E	0.834	0.99
38_R	41_A	0.816	0.98
14_E	83_L	0.814	0.98
81_D	102_P	0.802	0.98
29_P	44_S	0.797	0.98
92_V	101_I	0.789	0.98
40_V	43_V	0.788	0.98
3_V	12_V	0.788	0.98
69_Y	121_H	0.787	0.98
109_M	120_A	0.782	0.98
92_V	102_P	0.780	0.98
54_E	57_A	0.778	0.98
125_A	128_G	0.763	0.97
15_T	33_Y	0.762	0.97
22_L	25_G	0.752	0.97
88_G	92_V	0.750	0.97
69_Y	115_V	0.748	0.97
69_Y	132_N	0.746	0.97
87_A	91_P	0.742	0.97
6_P	11_A	0.736	0.97
58_R	61_A	0.727	0.97
5_C	38_R	0.727	0.97
53_R	56_E	0.721	0.96
13_V	124_H	0.695	0.96
73_H	105_G	0.695	0.96
77_L	114_R	0.694	0.96
57_A	67_A	0.693	0.96
67_A	70_A	0.691	0.95
7_C	36_C	0.679	0.95
62_D	66_A	0.679	0.95
55_M	115_V	0.678	0.95
99_P	102_P	0.670	0.95
11_A	38_R	0.666	0.94
114_R	121_H	0.665	0.94
63_P	66_A	0.665	0.94
120_A	134_V	0.657	0.94
51_G	55_M	0.655	0.94
56_E	109_M	0.652	0.94
53_R	57_A	0.651	0.94
16_A	88_G	0.642	0.93
91_P	99_P	0.638	0.93
106_A	109_M	0.638	0.93
76_Y	79_E	0.636	0.93
127_A	130_G	0.634	0.93
6_P	38_R	0.629	0.93
33_Y	40_V	0.625	0.92
33_Y	122_V	0.624	0.92
100_E	104_G	0.620	0.92
75_R	78_A	0.619	0.92
57_A	60_A	0.618	0.92
71_A	78_A	0.610	0.91
15_T	76_Y	0.608	0.91
86_A	92_V	0.602	0.91
62_D	68_A	0.602	0.91
13_V	33_Y	0.591	0.90
85_P	91_P	0.581	0.89
48_A	56_E	0.580	0.89
115_V	133_P	0.580	0.89
55_M	65_L	0.579	0.89
12_V	127_A	0.572	0.89
106_A	110_P	0.571	0.89
49_A	54_E	0.571	0.89
14_E	122_V	0.563	0.88
77_L	105_G	0.563	0.88
36_C	43_V	0.563	0.88
81_D	84_A	0.562	0.88
67_A	71_A	0.561	0.88
3_V	6_P	0.555	0.87
28_F	35_T	0.554	0.87
44_S	48_A	0.551	0.87
61_A	64_E	0.550	0.87
16_A	23_P	0.550	0.87
101_I	104_G	0.550	0.87
136_D	139_L	0.549	0.87
52_M	121_H	0.547	0.86
28_F	92_V	0.546	0.86
16_A	83_L	0.546	0.86
52_M	109_M	0.542	0.86
39_L	126_L	0.541	0.86
43_V	50_G	0.540	0.86
31_L	76_Y	0.540	0.86
132_N	135_G	0.540	0.86
110_P	114_R	0.540	0.86
59_L	66_A	0.539	0.86
32_Y	76_Y	0.535	0.85
25_G	91_P	0.530	0.85
69_Y	133_P	0.529	0.85
69_Y	72_A	0.525	0.84
53_R	113_D	0.525	0.84
72_A	124_H	0.524	0.84
5_C	39_L	0.519	0.83
34_L	48_A	0.518	0.83
109_M	121_H	0.518	0.83
56_E	60_A	0.517	0.83
32_Y	124_H	0.514	0.83
121_H	125_A	0.514	0.83
133_P	138_V	0.513	0.83
86_A	89_G	0.511	0.83
130_G	133_P	0.509	0.82
106_A	120_A	0.508	0.82
13_V	22_L	0.507	0.82
87_A	90_G	0.505	0.82
69_Y	109_M	0.500	0.81

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
1m0wA	2	0.9643	14	0.942	Contact Map
2bh9A	2	0.8286	12.3	0.943	Contact Map
4lgvA	4	0.7857	11.1	0.944	Contact Map
1xmaA	2	0.55	10.7	0.945	Contact Map
3ruiA	2	0.4357	10.7	0.945	Contact Map
2wyoA	2	0.9429	9.1	0.947	Contact Map
1hsjA	2	0.6357	8.8	0.947	Contact Map
3elkA	3	0.6286	8.7	0.947	Contact Map
2b3wA	1	0.8286	8.6	0.947	Contact Map
1uz3A	2	0.6571	8.4	0.947	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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